Preprints
Community incidence patterns drive the risk of SARS-CoV-2 outbreaks and alter intervention impacts in a high-risk institutional setting
SM Moore, G España, TA Perkins, RM Guido, JB Jucaban, TL Hall, ME Huhtanen, SA Peel, K Modjarrad, S Hakre, PT Scott
medRxiv doi:10.1101/2022.11.22.22282480
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An epidemiological and intervention assessment of the malaria epidemic in Bolivar, Venezuela: a modelling study
JH Huber, LF Chaves, AS Siraj, JE Moreno, ME Guevara, M Villegas, L Pocaterra, L Villegas, TA Perkins
medRxiv doi:10.1101/2022.04.19.22274042
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Ignoring transmission dynamics leads to underestimation of the impact of a novel intervention against mosquito-borne disease
SM Cavany*, JH Huber*, A Wieler, M Elliott, QM Tran, G España, SM Moore, TA Perkins
medRxiv doi:10.1101/2021.11.19.21266602
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Misdiagnosis prevents accurate monitoring of transmission and burden for sub-critical pathogens: a case study of Plasmodium knowlesi malaria
JH Huber
medRxiv doi:10.1101/2021.09.13.21263501
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The potential impact of delta variant of SARS-CoV-2 in the context of limited vaccination coverage and increasing social mixing in Bogotá, Colombia
G España, ZM Cucunubá, J Cuervo-Rojas, H Díaz, M González-Mayorga, JD Ramírez
medRxiv doi:10.1101/2021.08.06.21261734
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COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support
K Shea, RK Borchering, WJM Probert, E Howerton, TL Bogich, S Li, WG van Panhuis, C Viboud, R Aguas, A Belov, SH Bhargava, S Cavany, JC Chang, C Chen, J Chen, S Chen, YQ Chen, LM Childs, CC Chow, I Crooker, SY Del Valle, G España, G Fairchild, RC Gerkin, TC Germann, Q Gu, X Guan, L Guo, GR Hart, TJ Hladish, N Hupert, D Janies, CC Kerr, DJ Klein, E Klein, G Lin, C Manore, LA Meyers, J Mittler, K Mu, RC Nunez, R Oidtman, R Pasco, A Pastore y Pionti, R Paul, CAB Pearson, D Perdomo, TA Perkins, K Pierce, AN Pillai, RC Rael, K Rosenfeld, CW Ross, JA Spencer, AB Stoltzfus, KB Toh, S Vattikuti, A Vespignani, L Wang, L White, P Xu, Y Yang, ON Yogurtcu, W Zhang, Y Zhao, D Zou, M Ferrari, D Pannell, M Tildesley, J Seifarth, E Johnson, M Biggerstaff, M Johansson, RB Slayton, J Levander, J Stazer, J Salermo, MC Runge
medRxiv doi:10.1101/2020.11.03.20225409
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Ensemble forecasts of coronavirus disease 2019 (COVID-19) in the U.S.
EL Ray, N Wattanachit, J Niemi, AH Kanji, K House, EY Cramer, J Bracher, Andrew Zheng, TK Yamana, X Xiong, S Woody, Y Wang, L Wang, RL Walraven, V Tomar, K Sherratt, D Sheldon, RC Reiner, BA Prakash, D Osthus, ML Li, EC Lee, U Koyluoglu, P Keskinocak, Y Gu, Q Gu, GE George, G España, S Corsetti, J Chhatwal, S Cavany, H Biegel, M Ben-Nun, J Walker, R Slayton, V Lopez, M Biggerstaff, MA Johansson, NG Reich, COVID-19 Forecast Hub Consortium
medRxiv doi:10.1101/2020.08.19.20177493
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Social interventions can lower COVID-19 deaths in middle-income countries
A Paternina-Caicedo, M Choisy, C Garca-Calavaro, G España, J Rojas-Suarez, C Dueñas, A Smith, F De la Hoz Restrepo
medRxiv doi:10.1101/2020.04.16.20063727
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2023
Inapparent infections shape the transmission heterogeneity of dengue
GM Vazquez-Prokopec, AC Morrison, V Paz-Soldan, ST Stoddard, W Koval, LA Waller, TA Perkins, AL Lloyd, H Astete-Vega, J Elder, TW Scott, U Kitron
PNAS Nexus pgad024
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Spatial repellents: the current roadmap to global recommendation of spatial repellents for public health use
NL Achee, TA Perkins, SM Moore, F Liu, I Sagara, S Van Hulle, EO Ochomo, JE Gimnig, HA Tissera, SA Harvey, A Monroe, AC Morrison, TW Scott, RC Reiner Jr., JP Grieco
Current Research in Parasitology & Vector-Borne Diseases
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Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study
RK Borchering, LC Mulllany, E Howerton, M Chinazzi, CP Smith, M Qin, NG Reich, L Contamin, J Levander, J Kerr, J Espino, H Hochheiser, K Lovett, M Kinsey, K Tallaksen, S Wilson, L Shin, JC Lemaitre, JD Hulse, J Kaminsky, EC Lee, JT Davis, K Mu, X Xiong, A Pastore y Piontti, A Vespignani, A Srivastava, P Porebski, S Venkatramanan, A Adiga, B Lewis, B Klahn, J Outten, B Hurt, J Chen, H Mortveit, A Wilson, M Marathe, S Hoops, P Bhattacharya, D Machi, S Chen, R Paul, D Janies, JC Thill, M Galanti, T Yamana, S Pei, J Shaman, G España, S Cavany, S Moore, TA Perkins, JM Healy, RB Slayton, MA Johansson, M Biggerstaff, K Shea, SA Truelove, MC Runge, C Viboud, J Lessler
Lancet Regional Health - Americas 17:100398
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Expected endpoints from future chikungunya vaccine trial sites informed by serological data and modeling
QM Tran, KJ Soda, AS Siraj, SM Moore, HE Clapham, TA Perkins
Vaccine
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2022
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges
SM Cavany, C Barbera, M Carpenter, C Rodgers, T Sherman, M Stenglein, C Mayo, TA Perkins
Virus Evolution veac094
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Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
ML Poterek, CBF Vogels, ND Grubaugh, GD Ebel, TA Perkins, SM Cavany
Royal Society Open Science 9:220829
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The Remote Emerging Disease Intelligence—NETwork
NL Achee and the REDI-NET Consortium, including S Moore, S Mowry, TA Perkins, B Rodriguez
Frontiers in Microbiology
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Quantifying heterogeneities in arbovirus transmission: Description of the rationale and methodology for a prospective longitudinal study of dengue and Zika virus transmission in Iquitos, Peru (2014-2019)
AC Morrison, VA Paz-Soldan, GM Vazquez-Prokopec, L Lambrechts, WH Elson, P Barrera, H Astete, V Briesemeister, M Leguia, SA Jenkins, KC Long, AB Kawiecki, RC Reiner, TA Perkins, AL Lloyd, LA Waller, RD Hontz, ST Stoddard, CM Barker, U Kitron, JP Elder, AL Rothman, TW Scott
PLOS ONE
Prioritizing interventions for preventing COVID-19 outbreaks in military basic training
G España*, TA Perkins*, S Pollett, ME Smith, SM Moore, PO Kwon, TL Hall, MH Beagle Jr., CK Murray, S Hakre, S Peel, K Modjarrad, PT Scott
PLOS Computational Biology
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The impact of emerging Plasodium knowlesi on accurate diagnosis by light microscopy: a systematic review and modeling analysis
JH Huber, M Elliott, C Koepfli, TA Perkins
American Journal of Tropical Medicine and Hygiene
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Designing school reopening in the COVID-19 pre-vaccination period in Bogotá, Colombia: A modeling study
G España*, Z Cucunubá*, H Diaz, S Cavany, N Castañeda, L Rodriguez
PLOS Global Public Health 2:e0000467
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Projecting vaccine demand and impact for emerging zoonotic pathogens
A Lerch, QA ten Bosch, M L'Azou-Jackson, AA Bettis, M Bernuzzi, GAV Murphy, QM Tran, JH Huber, A Siraj, M Elliott, C Hartlage, K Koh, K Strimbu, M Walters, TA Perkins, SM Moore
BMC Medicine
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Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States
EY Cramer, EL Ray, VK Lopez, ... , 284 authors including S Cavany, G España, S Moore, R Oidtman, TA Perkins, ... , RB Slayton, MA Johansson, M Biggerstaff, NG Reich
Proceedings of the National Academy of Sciences 119:e2113561119
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Inferring person-to-person networks of pathogen transmission: is routine surveillance data up to the task?
JH Huber, MS Hsiang, N Dlamini, M Murphy, S Vilakati, N Nhlabathi, A Lerch, R Nielsen, N Ntshalintshali, B Greenhouse, TA Perkins
Malaria Journal 21:58
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Bluetongue research at a crossroads: modern genomics tools can pave the way to new insights
J Kopanke, M Carpenter, J Lee, K Reed, C Rodgers, M Burton, K Lovett, JA Westrich, E McNulty, E McDermott, C Barbera, S Cavany, JR Rohr, TA Perkins, CK Mathiason, M Stenglein, C Mayo
Annual Review of Animal Biosciences 10:303
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Performance of three molecular tests for SARS-CoV-2 on a university campus estimated jointly with Bayesian latent class modeling
TA Perkins, M Stephens, W Alvarez Barrios, SM Cavany, L Rulli, ME Pfrender
Microbiology Spectrum
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Inferring SARS-CoV-2 RNA shedding into wastewater relative to time of infection
SM Cavany, A Bivins, Z Wu, D North, K Bibby*, TA Perkins*
Epidemiology and Infection
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2021
Site-specific biases in phase-III clinical trials underestimate the effect of radical cure against Plasmodium vivax hypnozoites
JH Huber, C Koepfli, G España, N Nekkab, MT White, TA Perkins
Malaria Journal
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Timing is everything when it comes to pertussis vaccination
TA Perkins, QM Tran
Lancet Infectious Diseases
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The current burden of Japanese encephalitis and the estimated impacts of vaccination: Combining estimates of the spatial distribution and transmission intensity of a zoonotic pathogen
SM Moore
PLOS Neglected Tropical Diseases 15:e0009385
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Burden is in the eye of the beholder: sensitivity of yellow fever disease burden estimates to modeling assumptions
TA Perkins, JH Huber, QM Tran, RJ Oidtman, MK Walters, AS Siraj, SM Moore
Science Advances 7:eabg5033
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Trade-offs between individual and ensemble forecasts of an emerging infectious disease
RJ Oidtman, E Omodei, MUG Kraemer, CA Castaneda-Orjuela, E Cruz-Rivera, S Misnaza-Castrillon, MP Cifuentes, LE Rincon, V Canon, P de Alarcon, G España, JH Huber, SC Hill, CM Barker, MA Johansson, CA Manore, RC Reiner, I Rodriguez-Barraquer, AS Siraj, E Frias-Martinez, M Garcia-Herranz, TA Perkins
Nature Communications 12:5379
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Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA
G España, SM Cavany*, RJ Oidtman*, C Barbera, A Costello, A Lerch, M Poterek, Q Tran, A Wieler, S Moore, TA Perkins
Epidemics 37:100487
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Pre-preprint: August 21, 2020
Initial Twitter thread: August 21, 2020
Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world
J Toor, S Echeverria-Londono, X Li, K Abbas, ED Carter, HE Clapham, A Clark, MJ de Villiers, K Eilertson, M Ferrari, I Gamkrelidze, TB Hallett, WR Hinsley, D Hogan, JH Huber, ML Jackson, K Jean, M Jit, A Karachaliou, P Klepac, A Kraay, J Lessler, X Li, BA Lopman, T Mengistu, CJE Metcalf, SM Moore, S Nayagam, T Papadopoulos, TA Perkins, A Portnoy, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, Y Tam, H Tanvir, QM Tran, CL Trotter, SA Truelove, E Vynnycky, N Walker, A Winter, K Woodruff, NM Ferguson, KAM Gaythorpe
eLife 10:e67635
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The impact of dengue illness on social distancing and caregiving behavior
KL Schaber, AC Morrison, WH Elson, H Astete-Vega, JJ Córdova-López, EJ Ríos López, WL Quiroz Flores, AS Vizcarra Santillan, TW Scott, LA Waller, U Kitron, CM Barker, TA Perkins, AL Rothman, G Vazquez-Prokopec, JP Elder
PLOS Neglected Tropical Diseases
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Cost-effectiveness of dengue vaccination in Puerto Rico
G España, AJ Leidner, S Waterman, TA Perkins
PLOS Neglected Tropical Diseases
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Pandemic-associated mobility restrictions could cause increases in dengue virus transmission
SM Cavany, G España, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases
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Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries
K Gaythorpe*, K Abbas*, JH Huber*, A Karachaliou*, N Thakkar*, K Woodruff, X Li, S Echeverria-Londono, VIMC Working Group on COVID-19 Impact on Vaccine Preventable Disease, M Ferrari^, ML Jackson^, K McCarthy^, TA Perkins^, C Trotter^, M Jit^
eLife 10:e67023
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Over 100 years of Rift Valley fever: a patchwork of data on pathogen spread and spillover
GM Bron, K Strimbu, H Cecilia, A Lerch, SM Moore, Q Tran, TA Perkins, QA ten Bosch
Pathogens 10:708
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Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
AF Brito*, LC Machado*, RJ Oidtman*, MJL Siconelli*, QM Tran, JR Fauver, RD Carvalho, FZ Dezordi, MR Pereira, LA deCastro-Jorge, ECM Minto, LMR Passos, CC Kalinich, ME Petrone, E Allen, G España, AT Huang, DAT Cummings, G Baele, RFO Franca^, BAL da Fonseca^, TA Perkins^, GL Wallau^, ND Grubaugh^
Nature Communications 12:2619
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Co-circulation and misdiagnosis led to underestimation of the 2015-2017 Zika epidemic in the Americas
RJ Oidtman, G España, TA Perkins
PLOS Neglected Tropical Diseases 15:e0009208
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Air passenger travel and international surveillance data predict spatiotemporal variation in measles importations to the United States
M Poterek, MUG Kraemer, A Watts, K Khan, TA Perkins
Pathogens 10:155
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Dynamical characteristics of Covid-19 epidemic: Estimation from Colombia's case
H Diaz, G España, N Castañeda, L Rodriguez, F de la Hoz-Restrepo
International Journal of Infectious Diseases
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Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study
X Li, C Mukandavire, ZM Cucunubá, S Echeverria Londono, K Abbas, HE Clapham, M Jit, HL Johnson, T Papadopoulos, E Vynnycky, M Brisson, ED Carter, A Clark, MJ de Villliers, K Eilertson, MJ Ferrari, I Gamkrelidze, KAM Gaythorpe, NC Grassly, TB Hallett, W Hinsley, ML Jackson, K Jean, A Karachaliou, P Klepac, J Lessler, X Li, SM Moore, S Nayagam, DM Nguyen, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, S Sy, Y Tam, H Tanvir, QM Tran, CL Trotter, S Truelove, K van Zandvoort, S Verguet, N Walker, A Winter, K Woodruff, NM Ferguson, T Garske
Lancet 397:398-408
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Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics
KL Schaber, TA Perkins, AL Lloyd, LA Waller, U Kitron, VA Paz-Soldan, JP Elder, AL Rothman, DJ Civitello, WH Elson, AC Morrison, TW Scott, GM Vazquez-Prokopec
PLOS Computational Biology 17:e1008627
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2020
Hidden heterogeneity and its influence on dengue vaccination impact
MK Walters, TA Perkins
Infectious Disease Modelling 5:783
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Seven challenges for spatial analyses of vector-borne diseases
TA Perkins, G España, SM Moore, RJ Oidtman, S Sharma, B Singh, AS Siraj, KJ Soda, M Smith, MK Walters, E Michael
In: Population Biology of Vector-Borne Diseases (Drake, Bonsall, Strand eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas
SM Moore, RJ Oidtman, KJ Soda, AS Siraj, RC Reiner, Jr., CM Barker, TA Perkins
PLOS Neglected Tropical Diseases 14:e0008640
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Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes
QA ten Bosch, JM Wagman, F Castro-Llanos, NL Achee, JP Grieco, TA Perkins
PLOS Computational Biology 16:e1008190
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Optimal control of the COVID-19 pandemic with non-pharmaceutical interventions
TA Perkins, G España
Bulletin of Mathematical Biology 82:118
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Pre-preprint: April 21, 2020
Initial Twitter thread: April 21, 2020
Estimating unobserved SARS-CoV-2 infections in the United States
TA Perkins*, SM Cavany*, SM Moore*, RJ Oidtman, A Lerch, M Poterek
Proceedings of the National Academy of Sciences
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Pre-preprint: March 15, 2020
Initial code shared: March 12, 2020
Initial Twitter thread: March 10, 2020
Theories of diversity in disease ecology
TA Perkins, JR Rohr
In: Theoretical Ecology: Concepts and Applications (McCann and Gellner, eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Malaria elimination in Costa Rica: changes in treatment and mass drug administration
LF Chaves, JH Huber, O Rojas Salas, M Ramirez Rojas, LM Romero, JM Gutierrez Alvarado, TA Perkins, M Prado, RM Rodriguez
Microorganisms 8:984
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Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19
A Bivins, D North, A Ahmad, W Ahmed, E Alm, F Been, P Bhattacharya, L Bijlsma, AB Boehm, J Brown, G Buttiglieri, V Calabro, A Carducci, A Castiglioni, Z Gurol, S Chakraborty, F Costa, S Curcio, F de los Reyes, J Vela, K Farkas, X Fernandez-Casi, C Gerba, D Gerrity, R Girones, R Gonzalez, E Haramoto, A Harris, P Holden, M Islam, D Jones, B Kasprzyk-Hordern, M Kitajima, N Kotlarz, M Kumar, K Kuroda, G La Rosa, F Malpei, M Mautus, S McLellan, G Medema, J Meschke, J Mueller, R Newton, D Nilsson, R Noble, A van Nuijs, J Peccia, TA Perkins, A Pickering, J Rose, G Sanchez, A Smith, L Stadler, C Stauber, K Thomas, T van der Voorn, K Wigginton, K Zhu, K Bibby
Environmental Science and Technology
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Mapping global variation in human mobility
MUG Kraemer, A Sadilek, Q Zhang, NA Marchal, G Tuli, EL Cohn, Y Hswen, TA Perkins, DL Smith, RC Reiner, JS Brownstein
Nature Human Behavior
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Modeling human migration across spatial scales in Colombia
AS Siraj, A Sorichetta, G España, AJ Tatem, TA Perkins
PLOS ONE 15:e0232702
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Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response
SM Cavany, G España, AL Lloyd, LA Waller, U Kitron, H Astete, WH Elson, GM Vazquez-Prokopec, TW Scott, AC Morrison, RC Reiner Jr., TA Perkins
PLOS Computational Biology 16:e1007743
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Ecological dynamics impacting bluetongue virus transmission in North America
CE Mayo, EG McDermott, J Kopanke, M Stenglein, J Lee, C Mathiason, M Carpenter, K Reed, TA Perkins
Frontiers in Veterinary Science
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Aggregated mobility data could help fight COVID-19
CO Buckee, S Balsari, J Chan, M Crosas, F Dominici, U Gasser, YH Grad, B Grenfell, ME Halloran, MUG Kraemer, M Lipsitch, CJE Metcalf, LA Meyers, TA Perkins, M Santillana, SV Scarpino, C Viboud, A Wesolowski, A Schroeder
Science doi:10.1126/eabb8021
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The basic reproductive number for disease systems with multiple coupled heterogeneities
A Lloyd, U Kitron, TA Perkins, GM Vazquez-Prokopec, L Waller
Mathematical Biosciences 321:108294
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2019
Dengue illness impacts daily human mobility patterns in Iquitos, Peru
KL Schaber, VA Paz-Soldan, AC Morrison, WHD Elson, AL Rothman, CN Mores, H Astete-Vega, TW Scott, LA Waller, U Kitron, JP Elder, CM Barker, TA Perkins, GM Vazquez-Prokopec
PLOS Neglected Tropical Diseases 13:e0007756
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Pre-vaccination screening strategies for the use of the CYD-TDV dengue vaccine: a meeting report
A Wilder-Smith, PG Smith, R Luo, C Kelly-Cirino, D Curry, H Larson, A Durbin, M Chu, P Tharmaphornpilas, LC Ng, AMC Sartori, EJA Luna, DJ Gubler, G España, IK Yoon, S Flasche
Vaccine 37 5137-5146
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Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic
N Grubaugh, S Saraf, K Gangavarapu, A Watts, AL Tan, RJ Oidtman, JT Ladner, G Oliveira, NL Matteson, MUG Kraemer, CBF Vogels, A Hentoff, D Bhatia, D Stanek, B Scott, V Landis, I Stryker, M Cone, E Kopp, A Cannons, L Heberlein-Larson, S White, L Gillis, M Ricciardi, J Kwal, P Lichtenberger, D Magnani, D Watkins, G Palacios, DH Hamer, GeoSentinel Surveillance Network, L Gardner, TA Perkins, G Baele, K Khan, A Morrison, S Isern, SF Michael, KG Andersen
Cell 178:1057-1071 doi:10.1016/j.cell.2019.07.018
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Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data
TA Perkins*, I Rodriguez-Barraquer*, C Manore*, AS Siraj, G España, CM Barker, MA Johansson, RC Reiner, Jr.*
Epidemics 100357
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Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure
G España, Y Yao, KB Anderson, MC Fitzpatrick, DL Smith, AC Morrison, A Wilder-Smith, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases 13:e0007482
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Downgrading disease transmission risk estimates using terminal importations
SJ Fox, SE Bellan, TA Perkins, MA Johansson, LA Meyers
PLOS Neglected Tropical Diseases 13:e0007395
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Estimating the impact of city-wide Aedes aegypti population control: an observational study in Iquitos, Peru
RC Reiner, Jr., S Stoddard, G Vazquez-Prokopec, H Astete, TA Perkins, M Sihuincha, J Stancil, DL Smith, T Kochel, E Halsey, U Kitron, AC Morrison, TW Scott
PLOS Neglected Tropical Diseases 13:e0007255
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An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
TA Perkins*, RC Reiner, Jr.*, G España*, QA ten Bosch, A Verma, K Liebman, VA Paz-Soldan, JP Elder, AC Morrison, ST Stoddard, U Kitron, GM Vazquez-Prokopec, TW Scott, DL Smith
PLOS Computational Biology 15:e1006710
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Inter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China
RJ Oidtman, S Lai, Z Huang, J Yang, AS Siraj, RC Reiner, Jr., AJ Tatem, TA Perkins, H Yu
Nature Communications 10:1148
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Spatial sorting as the spatial analogue of natural selection
BL Phillips, TA Perkins
Theoretical Ecology 12:155-163
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Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus
MUG Kraemer*, RC Reiner, Jr.*, OJ Brady*, JP Messina*, M Gilbert*, DM Pigott, D Yi, K Johnson, L Earl, LB Marczak, S Shirude, ND Weaver, D Bisanzio, TA Perkins, S Lai, X Lu, P Jones, GE Coelho, RG Carvalho, W Van Bortel, C Marsboom, G Hendrickx, F Schaffner, CG Moore, HH Nax, L Bengtsson, E Wetter, AJ Tatem, JS Brownstein, DL Smith, L Lambrechts, S Cauchemez, C Linard, NR Faria, OG Pybus, TW Scott, Q Liu, H Yu, GRW Wint, SI Hay, N Golding
Nature Microbiology
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Letter to the editor in response to 'Reconstruction and prediction of viral disease epidemics'
TA Perkins
Epidemiology and Infection 147:398
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Biased efficacy estimates in phase-III dengue vaccine trials due to heterogeneous exposure and differential detectability of primary infections across trial arms
G España, C Hogea, A Guignard, QA ten Bosch, AC Morrison, DL Smith, TW Scott, A Schmidt, TA Perkins
PLOS ONE 14:e0210041
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Arbovirus coinfection and co-transmission: a neglected public health concern?
CBF Vogels*, C Ruckert*, SM Cavany*, TA Perkins, GD Ebel, ND Grubaugh
PLOS Biology 17:e3000130
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2018
Mapping malaria by combining parasite genomic and epidemiologic data
A Wesolowski, A Taylor, H-H Chang, R Verity, S Tessema, J Bailey, TA Perkins, D Neafsey, B Greenhouse, CO Buckee
BMC Medicine 16:190
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Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity
SM Moore, QA ten Bosch, AS Siraj, KJ Soda, G España, A Campo, S Gómez, D Salas, B Raybaud, E Wenger, P Welkhoff, TA Perkins
BMC Medicine 16:152
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Exploring scenarios of chikungunya mitigation with a data-driven agent-based model of the 2014-2016 outbreak in Colombia
G España, J Grefenstette, TA Perkins, C Torres, A Campo Carey, H Diaz, F de la Hoz, DS Burke, WG van Panhuis
Scientific Reports 8:12201
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Implementation and applications of EMOD, an individual-based multi-disease modeling platform
A Bershtyn, J Gerardin, D Bridenbecker, CW Lorton, J Bloedow, RS Baker, G Chabot-Couture, Y Chen, T Fischle, K Frey, JS Gauld, H Hu, AS Izzo, DJ Klein, D Lukacevic, KA McCarthy, JC Miller, AL Ouedraogo, TA Perkins, J Steinkraus, QA ten Bosch, HF Ting, S Titova, BG Wagner, PA Welkhoff, EA Wenger, CN Wiswell
Pathogens and Disease 76:fty059
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Model-based analysis of experimental data from interconnected, row-configured huts elucidates multifaceted effects of a volatile chemical on Aedes aegypti mosquitoes
QA ten Bosch, F Castro-Llanos, H Manda, AC Morrison, JP Grieco, NL Achee, TA Perkins
Parasites and Vectors 11:365
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Inferences about spatiotemporal variation in dengue virus transmission are sensitive to assumptions about human mobility: a case study using geolocated tweets from Lahore, Pakistan
MUG Kraemer, D Bisanzio, RC Reiner, Jr., R Zakar, JB Hawkins, CC Freifeld, DL Smith, SI Hay, JS Brownstein, TA Perkins
EPJ Data Science 7:16
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Contributions from the silent majority dominate dengue virus transmission
QA ten Bosch, HE Clapham, L Lambrechts, V Duoung, P Buchy, BM Althouse, AL Loyd, LA Waller, AC Morrison, U Kitron, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Pathogens 14:e1006965
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Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia
AS Siraj, I Rodriguez-Barraquer, CM Barker, N Tejedor-Garavito, D Harding, C Lorton, D Lukacevic, G Oates, G España, MUG Kraemer, C Manore, MA Johansson, AJ Tatem, RC Reiner, Jr., TA Perkins
Scientific Data 5:180073
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DTK-Dengue: A new agent-based model of dengue virus transmission dynamics
KJ Soda, SM Moore, G España, J Bloedow, B Raybaud, B Althouse, MA Johansson, E Wenger, P Welkhoff, TA Perkins*, QA ten Bosch*
bioRxiv doi:10.1101/376533
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2017
Assessing the population at risk of Zika virus in Asia - is the emergency really over?
AS Siraj, TA Perkins
BMJ Global Health 2:e000309
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Temperature modulates dengue virus epidemic growth rates through its effects on reproduction numbers and generation intervals
AS Siraj, RJ Oidtman, JH Huber, MUG Kraemer, OJ Brady, MA Johansson, TA Perkins
PLOS Neglected Tropical Diseases 11:e0005797
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Retracing Zika's footsteps across the Americas with computational modeling
TA Perkins
Proceedings of the National Academy of Sciences 114:5558-5560
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Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017
Zika Modeling and Projections for Vaccination Trials Collaboration (in alphabetical order): J Asher, C Barker, G Chen, D Cummings, M Chinazzi, S Daniel-Wyman, M Fischer, N Ferguson, D Follman, ME Halloran, M Johansson, K Kugeler, J Kwan, J Lessler, IM Longini, S Merler, A Monaghan, A Pastore y Piontti, TA Perkins, DR Prevots, RC Reiner, Jr., L Rossi, I Rodriguez-Barraquer, AS Siraj, K Sun, A Vespignanni, Q Zhang
bioRxiv doi:10.1101/187591
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2016
The long-term safety, public health impact, and cost-effectiveness of routine vaccination with a recombinant, live-attenuated dengue vaccine (Dengvaxia): A model comparison study
S Flasche*, M Jit*, I Rodriguez-Barraquer*, L Coudeville*, M Recker*, K Koelle*, G Milne*, TJ Hladish*, TA Perkins*, DAT Cummings, I Dorigatti, DJ Laydon, G España, J Kelso, I Longini, J Lourenco, CAB Pearson, RC Reiner, Jr., L Mier-y-Teran-Romero, K Vannice, N Ferguson
PLOS Medicine 13:e1002181
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Pokemon Go and exposure to mosquito-borne diseases: How not to catch 'em all
RJ Oidtman, RC Christofferson, QA ten Bosch, G España, MUG Kraemer, AJ Tatem, CM Barker, TA Perkins
PLOS Currents Outbreaks
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Quantitative, model-based estimates of variability in the generation and serial intervals of Plasmodium falciparum malaria
JH Huber, GL Johnston, B Greenhouse, DL Smith, TA Perkins
Malaria Journal 15:490
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After the games are over: life-history trade-offs drive dispersal attenuation following range expansion
TA Perkins, C Boettiger, BL Phillips
Ecology and Evolution doi:10.1002/ece3.2314
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Model-based projections of Zika virus infections in childbearing women in the Americas
TA Perkins, AS Siraj, C Warren Ruktanonchai, MUG Kraemer, AJ Tatem
Nature Microbiology 1:16126
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Calling in sick: impacts of fever on intra-urban human mobility
TA Perkins, VA Paz Soldan, ST Stoddard, AC Morrison, BM Forshey, KC Long, ES Halsey, TJ Kochel, JP Elder, U Kitron, TW Scott, GM Vazquez-Prokopec
Proceedings of the Royal Society B 283:20160390
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Quantifying the epidemiological impact of vector control on dengue
RC Reiner, Jr., N Achee, R Barrera, TR Burkot, DD Chadee, G Devine, T Endy, D Gubler, J Homback, I Kleinschmidt, A Lenhart, S Lindsay, I Longini, M Mondy, AC Morrison, TA Perkins, GM Vazquez-Prokopec, P Reiter, S Ritchie, DL Smith, D Strickman, TW Scott
PLOS Neglected Tropical Diseases 10:e0004588
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Coupled heterogeneities and their impact on parasite transmission and control
GM Vazquez-Prokopeck, TA Perkins, LA Waller, AL Lloyd, RC Reiner, Jr., TW Scott, U Kitron
Trends in Parasitology 32:356-367
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Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, ME Sinka, CL Moyes, PA Eckhoff, TW Scott, SW Lindsay, SI Hay, DL Smith
Transactions of the Royal Society of Tropical Medicine and Hygiene 110:107-117
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2015
Mapping residual transmission for malaria elimination
RC Reiner, Jr., A Le Menach, S Kunene, N Ntshalintshali, M Hsiang, TA Perkins, B Greenhouse, AJ Tatem, JM Cohen, DL Smith
eLife 4:e09520
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Big city, small world: density, contact rates, and transmission of dengue across Pakistan
MUG Kraemer, TA Perkins, DAT Cummings, R Zakar, SI Hay, DL Smith, RC Reiner, Jr.
Journal of the Royal Society Interface 12:20150468
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A critical assessment of vector control for dengue prevention
NL Achee, F Gould, TA Perkins, RC Reiner, Jr., AC Morrison, SA Ritchie, DJ Gubler, R Teyssou, TW Scott
PLOS Neglected Tropical Diseases 9:e0003655
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The changing epidemiology of dengue in China, 1990-2014: a descriptive analysis of 25 years of nationwide surveillance data
S Lai, Z Huang, H Zhou, KL Anders, TA Perkins, W Yin, Y Li, D Mu, Q Chen, Z Zhang, Y Qiu, L Wang, H Zhang, L Zeng, X Ren, M Geng, Z Li, AJ Tatem, SI Hay, H Yu
BMC Medicine 13:100
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Adult vector control, mosquito ecology, and malaria transmission
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, TW Scott, SW Lindsay, SI Hay, DL Smith
International Health 7:121-129
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Estimating drivers of autochthonous transmission of chikungunya virus in its invasion of the Americas
TA Perkins, CJE Metcalf, BT Grenfell, AJ Tatem
PLOS Currents Outbreaks
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2014 and before
See Alex's Google Scholar page for a list of his publications prior to forming his lab at Notre Dame.
Community incidence patterns drive the risk of SARS-CoV-2 outbreaks and alter intervention impacts in a high-risk institutional setting
SM Moore, G España, TA Perkins, RM Guido, JB Jucaban, TL Hall, ME Huhtanen, SA Peel, K Modjarrad, S Hakre, PT Scott
medRxiv doi:10.1101/2022.11.22.22282480
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An epidemiological and intervention assessment of the malaria epidemic in Bolivar, Venezuela: a modelling study
JH Huber, LF Chaves, AS Siraj, JE Moreno, ME Guevara, M Villegas, L Pocaterra, L Villegas, TA Perkins
medRxiv doi:10.1101/2022.04.19.22274042
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Ignoring transmission dynamics leads to underestimation of the impact of a novel intervention against mosquito-borne disease
SM Cavany*, JH Huber*, A Wieler, M Elliott, QM Tran, G España, SM Moore, TA Perkins
medRxiv doi:10.1101/2021.11.19.21266602
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Misdiagnosis prevents accurate monitoring of transmission and burden for sub-critical pathogens: a case study of Plasmodium knowlesi malaria
JH Huber
medRxiv doi:10.1101/2021.09.13.21263501
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The potential impact of delta variant of SARS-CoV-2 in the context of limited vaccination coverage and increasing social mixing in Bogotá, Colombia
G España, ZM Cucunubá, J Cuervo-Rojas, H Díaz, M González-Mayorga, JD Ramírez
medRxiv doi:10.1101/2021.08.06.21261734
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COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support
K Shea, RK Borchering, WJM Probert, E Howerton, TL Bogich, S Li, WG van Panhuis, C Viboud, R Aguas, A Belov, SH Bhargava, S Cavany, JC Chang, C Chen, J Chen, S Chen, YQ Chen, LM Childs, CC Chow, I Crooker, SY Del Valle, G España, G Fairchild, RC Gerkin, TC Germann, Q Gu, X Guan, L Guo, GR Hart, TJ Hladish, N Hupert, D Janies, CC Kerr, DJ Klein, E Klein, G Lin, C Manore, LA Meyers, J Mittler, K Mu, RC Nunez, R Oidtman, R Pasco, A Pastore y Pionti, R Paul, CAB Pearson, D Perdomo, TA Perkins, K Pierce, AN Pillai, RC Rael, K Rosenfeld, CW Ross, JA Spencer, AB Stoltzfus, KB Toh, S Vattikuti, A Vespignani, L Wang, L White, P Xu, Y Yang, ON Yogurtcu, W Zhang, Y Zhao, D Zou, M Ferrari, D Pannell, M Tildesley, J Seifarth, E Johnson, M Biggerstaff, M Johansson, RB Slayton, J Levander, J Stazer, J Salermo, MC Runge
medRxiv doi:10.1101/2020.11.03.20225409
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Ensemble forecasts of coronavirus disease 2019 (COVID-19) in the U.S.
EL Ray, N Wattanachit, J Niemi, AH Kanji, K House, EY Cramer, J Bracher, Andrew Zheng, TK Yamana, X Xiong, S Woody, Y Wang, L Wang, RL Walraven, V Tomar, K Sherratt, D Sheldon, RC Reiner, BA Prakash, D Osthus, ML Li, EC Lee, U Koyluoglu, P Keskinocak, Y Gu, Q Gu, GE George, G España, S Corsetti, J Chhatwal, S Cavany, H Biegel, M Ben-Nun, J Walker, R Slayton, V Lopez, M Biggerstaff, MA Johansson, NG Reich, COVID-19 Forecast Hub Consortium
medRxiv doi:10.1101/2020.08.19.20177493
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Social interventions can lower COVID-19 deaths in middle-income countries
A Paternina-Caicedo, M Choisy, C Garca-Calavaro, G España, J Rojas-Suarez, C Dueñas, A Smith, F De la Hoz Restrepo
medRxiv doi:10.1101/2020.04.16.20063727
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2023
Inapparent infections shape the transmission heterogeneity of dengue
GM Vazquez-Prokopec, AC Morrison, V Paz-Soldan, ST Stoddard, W Koval, LA Waller, TA Perkins, AL Lloyd, H Astete-Vega, J Elder, TW Scott, U Kitron
PNAS Nexus pgad024
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Spatial repellents: the current roadmap to global recommendation of spatial repellents for public health use
NL Achee, TA Perkins, SM Moore, F Liu, I Sagara, S Van Hulle, EO Ochomo, JE Gimnig, HA Tissera, SA Harvey, A Monroe, AC Morrison, TW Scott, RC Reiner Jr., JP Grieco
Current Research in Parasitology & Vector-Borne Diseases
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Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study
RK Borchering, LC Mulllany, E Howerton, M Chinazzi, CP Smith, M Qin, NG Reich, L Contamin, J Levander, J Kerr, J Espino, H Hochheiser, K Lovett, M Kinsey, K Tallaksen, S Wilson, L Shin, JC Lemaitre, JD Hulse, J Kaminsky, EC Lee, JT Davis, K Mu, X Xiong, A Pastore y Piontti, A Vespignani, A Srivastava, P Porebski, S Venkatramanan, A Adiga, B Lewis, B Klahn, J Outten, B Hurt, J Chen, H Mortveit, A Wilson, M Marathe, S Hoops, P Bhattacharya, D Machi, S Chen, R Paul, D Janies, JC Thill, M Galanti, T Yamana, S Pei, J Shaman, G España, S Cavany, S Moore, TA Perkins, JM Healy, RB Slayton, MA Johansson, M Biggerstaff, K Shea, SA Truelove, MC Runge, C Viboud, J Lessler
Lancet Regional Health - Americas 17:100398
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Expected endpoints from future chikungunya vaccine trial sites informed by serological data and modeling
QM Tran, KJ Soda, AS Siraj, SM Moore, HE Clapham, TA Perkins
Vaccine
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2022
Modeling cellular co-infection and reassortment of bluetongue virus in Culicoides midges
SM Cavany, C Barbera, M Carpenter, C Rodgers, T Sherman, M Stenglein, C Mayo, TA Perkins
Virus Evolution veac094
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Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
ML Poterek, CBF Vogels, ND Grubaugh, GD Ebel, TA Perkins, SM Cavany
Royal Society Open Science 9:220829
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The Remote Emerging Disease Intelligence—NETwork
NL Achee and the REDI-NET Consortium, including S Moore, S Mowry, TA Perkins, B Rodriguez
Frontiers in Microbiology
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Quantifying heterogeneities in arbovirus transmission: Description of the rationale and methodology for a prospective longitudinal study of dengue and Zika virus transmission in Iquitos, Peru (2014-2019)
AC Morrison, VA Paz-Soldan, GM Vazquez-Prokopec, L Lambrechts, WH Elson, P Barrera, H Astete, V Briesemeister, M Leguia, SA Jenkins, KC Long, AB Kawiecki, RC Reiner, TA Perkins, AL Lloyd, LA Waller, RD Hontz, ST Stoddard, CM Barker, U Kitron, JP Elder, AL Rothman, TW Scott
PLOS ONE
Prioritizing interventions for preventing COVID-19 outbreaks in military basic training
G España*, TA Perkins*, S Pollett, ME Smith, SM Moore, PO Kwon, TL Hall, MH Beagle Jr., CK Murray, S Hakre, S Peel, K Modjarrad, PT Scott
PLOS Computational Biology
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The impact of emerging Plasodium knowlesi on accurate diagnosis by light microscopy: a systematic review and modeling analysis
JH Huber, M Elliott, C Koepfli, TA Perkins
American Journal of Tropical Medicine and Hygiene
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Designing school reopening in the COVID-19 pre-vaccination period in Bogotá, Colombia: A modeling study
G España*, Z Cucunubá*, H Diaz, S Cavany, N Castañeda, L Rodriguez
PLOS Global Public Health 2:e0000467
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Projecting vaccine demand and impact for emerging zoonotic pathogens
A Lerch, QA ten Bosch, M L'Azou-Jackson, AA Bettis, M Bernuzzi, GAV Murphy, QM Tran, JH Huber, A Siraj, M Elliott, C Hartlage, K Koh, K Strimbu, M Walters, TA Perkins, SM Moore
BMC Medicine
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Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States
EY Cramer, EL Ray, VK Lopez, ... , 284 authors including S Cavany, G España, S Moore, R Oidtman, TA Perkins, ... , RB Slayton, MA Johansson, M Biggerstaff, NG Reich
Proceedings of the National Academy of Sciences 119:e2113561119
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Inferring person-to-person networks of pathogen transmission: is routine surveillance data up to the task?
JH Huber, MS Hsiang, N Dlamini, M Murphy, S Vilakati, N Nhlabathi, A Lerch, R Nielsen, N Ntshalintshali, B Greenhouse, TA Perkins
Malaria Journal 21:58
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Bluetongue research at a crossroads: modern genomics tools can pave the way to new insights
J Kopanke, M Carpenter, J Lee, K Reed, C Rodgers, M Burton, K Lovett, JA Westrich, E McNulty, E McDermott, C Barbera, S Cavany, JR Rohr, TA Perkins, CK Mathiason, M Stenglein, C Mayo
Annual Review of Animal Biosciences 10:303
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Performance of three molecular tests for SARS-CoV-2 on a university campus estimated jointly with Bayesian latent class modeling
TA Perkins, M Stephens, W Alvarez Barrios, SM Cavany, L Rulli, ME Pfrender
Microbiology Spectrum
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Inferring SARS-CoV-2 RNA shedding into wastewater relative to time of infection
SM Cavany, A Bivins, Z Wu, D North, K Bibby*, TA Perkins*
Epidemiology and Infection
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2021
Site-specific biases in phase-III clinical trials underestimate the effect of radical cure against Plasmodium vivax hypnozoites
JH Huber, C Koepfli, G España, N Nekkab, MT White, TA Perkins
Malaria Journal
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Timing is everything when it comes to pertussis vaccination
TA Perkins, QM Tran
Lancet Infectious Diseases
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The current burden of Japanese encephalitis and the estimated impacts of vaccination: Combining estimates of the spatial distribution and transmission intensity of a zoonotic pathogen
SM Moore
PLOS Neglected Tropical Diseases 15:e0009385
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Burden is in the eye of the beholder: sensitivity of yellow fever disease burden estimates to modeling assumptions
TA Perkins, JH Huber, QM Tran, RJ Oidtman, MK Walters, AS Siraj, SM Moore
Science Advances 7:eabg5033
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Trade-offs between individual and ensemble forecasts of an emerging infectious disease
RJ Oidtman, E Omodei, MUG Kraemer, CA Castaneda-Orjuela, E Cruz-Rivera, S Misnaza-Castrillon, MP Cifuentes, LE Rincon, V Canon, P de Alarcon, G España, JH Huber, SC Hill, CM Barker, MA Johansson, CA Manore, RC Reiner, I Rodriguez-Barraquer, AS Siraj, E Frias-Martinez, M Garcia-Herranz, TA Perkins
Nature Communications 12:5379
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Impacts of K-12 school reopening on the COVID-19 epidemic in Indiana, USA
G España, SM Cavany*, RJ Oidtman*, C Barbera, A Costello, A Lerch, M Poterek, Q Tran, A Wieler, S Moore, TA Perkins
Epidemics 37:100487
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Pre-preprint: August 21, 2020
Initial Twitter thread: August 21, 2020
Lives saved with vaccination for 10 pathogens across 112 countries in a pre-COVID-19 world
J Toor, S Echeverria-Londono, X Li, K Abbas, ED Carter, HE Clapham, A Clark, MJ de Villiers, K Eilertson, M Ferrari, I Gamkrelidze, TB Hallett, WR Hinsley, D Hogan, JH Huber, ML Jackson, K Jean, M Jit, A Karachaliou, P Klepac, A Kraay, J Lessler, X Li, BA Lopman, T Mengistu, CJE Metcalf, SM Moore, S Nayagam, T Papadopoulos, TA Perkins, A Portnoy, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, Y Tam, H Tanvir, QM Tran, CL Trotter, SA Truelove, E Vynnycky, N Walker, A Winter, K Woodruff, NM Ferguson, KAM Gaythorpe
eLife 10:e67635
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The impact of dengue illness on social distancing and caregiving behavior
KL Schaber, AC Morrison, WH Elson, H Astete-Vega, JJ Córdova-López, EJ Ríos López, WL Quiroz Flores, AS Vizcarra Santillan, TW Scott, LA Waller, U Kitron, CM Barker, TA Perkins, AL Rothman, G Vazquez-Prokopec, JP Elder
PLOS Neglected Tropical Diseases
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Cost-effectiveness of dengue vaccination in Puerto Rico
G España, AJ Leidner, S Waterman, TA Perkins
PLOS Neglected Tropical Diseases
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Pandemic-associated mobility restrictions could cause increases in dengue virus transmission
SM Cavany, G España, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases
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Impact of COVID-19-related disruptions to measles, meningococcal A, and yellow fever vaccination in 10 countries
K Gaythorpe*, K Abbas*, JH Huber*, A Karachaliou*, N Thakkar*, K Woodruff, X Li, S Echeverria-Londono, VIMC Working Group on COVID-19 Impact on Vaccine Preventable Disease, M Ferrari^, ML Jackson^, K McCarthy^, TA Perkins^, C Trotter^, M Jit^
eLife 10:e67023
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Over 100 years of Rift Valley fever: a patchwork of data on pathogen spread and spillover
GM Bron, K Strimbu, H Cecilia, A Lerch, SM Moore, Q Tran, TA Perkins, QA ten Bosch
Pathogens 10:708
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Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
AF Brito*, LC Machado*, RJ Oidtman*, MJL Siconelli*, QM Tran, JR Fauver, RD Carvalho, FZ Dezordi, MR Pereira, LA deCastro-Jorge, ECM Minto, LMR Passos, CC Kalinich, ME Petrone, E Allen, G España, AT Huang, DAT Cummings, G Baele, RFO Franca^, BAL da Fonseca^, TA Perkins^, GL Wallau^, ND Grubaugh^
Nature Communications 12:2619
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Co-circulation and misdiagnosis led to underestimation of the 2015-2017 Zika epidemic in the Americas
RJ Oidtman, G España, TA Perkins
PLOS Neglected Tropical Diseases 15:e0009208
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Air passenger travel and international surveillance data predict spatiotemporal variation in measles importations to the United States
M Poterek, MUG Kraemer, A Watts, K Khan, TA Perkins
Pathogens 10:155
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Dynamical characteristics of Covid-19 epidemic: Estimation from Colombia's case
H Diaz, G España, N Castañeda, L Rodriguez, F de la Hoz-Restrepo
International Journal of Infectious Diseases
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Estimating the health impact of vaccination against ten pathogens in 98 low-income and middle-income countries from 2000 to 2030: a modelling study
X Li, C Mukandavire, ZM Cucunubá, S Echeverria Londono, K Abbas, HE Clapham, M Jit, HL Johnson, T Papadopoulos, E Vynnycky, M Brisson, ED Carter, A Clark, MJ de Villliers, K Eilertson, MJ Ferrari, I Gamkrelidze, KAM Gaythorpe, NC Grassly, TB Hallett, W Hinsley, ML Jackson, K Jean, A Karachaliou, P Klepac, J Lessler, X Li, SM Moore, S Nayagam, DM Nguyen, H Razavi, D Razavi-Shearer, S Resch, C Sanderson, S Sweet, S Sy, Y Tam, H Tanvir, QM Tran, CL Trotter, S Truelove, K van Zandvoort, S Verguet, N Walker, A Winter, K Woodruff, NM Ferguson, T Garske
Lancet 397:398-408
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Disease-driven reduction in human mobility influences human-mosquito contacts and dengue transmission dynamics
KL Schaber, TA Perkins, AL Lloyd, LA Waller, U Kitron, VA Paz-Soldan, JP Elder, AL Rothman, DJ Civitello, WH Elson, AC Morrison, TW Scott, GM Vazquez-Prokopec
PLOS Computational Biology 17:e1008627
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2020
Hidden heterogeneity and its influence on dengue vaccination impact
MK Walters, TA Perkins
Infectious Disease Modelling 5:783
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Seven challenges for spatial analyses of vector-borne diseases
TA Perkins, G España, SM Moore, RJ Oidtman, S Sharma, B Singh, AS Siraj, KJ Soda, M Smith, MK Walters, E Michael
In: Population Biology of Vector-Borne Diseases (Drake, Bonsall, Strand eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Leveraging multiple data types to estimate the size of the Zika epidemic in the Americas
SM Moore, RJ Oidtman, KJ Soda, AS Siraj, RC Reiner, Jr., CM Barker, TA Perkins
PLOS Neglected Tropical Diseases 14:e0008640
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Community-level impacts of spatial repellents for control of diseases vectored by Aedes aegypti mosquitoes
QA ten Bosch, JM Wagman, F Castro-Llanos, NL Achee, JP Grieco, TA Perkins
PLOS Computational Biology 16:e1008190
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Optimal control of the COVID-19 pandemic with non-pharmaceutical interventions
TA Perkins, G España
Bulletin of Mathematical Biology 82:118
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Pre-preprint: April 21, 2020
Initial Twitter thread: April 21, 2020
Estimating unobserved SARS-CoV-2 infections in the United States
TA Perkins*, SM Cavany*, SM Moore*, RJ Oidtman, A Lerch, M Poterek
Proceedings of the National Academy of Sciences
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Pre-preprint: March 15, 2020
Initial code shared: March 12, 2020
Initial Twitter thread: March 10, 2020
Theories of diversity in disease ecology
TA Perkins, JR Rohr
In: Theoretical Ecology: Concepts and Applications (McCann and Gellner, eds.)
Oxford University Press
link to purchase the book | email Alex for a chapter pdf
Malaria elimination in Costa Rica: changes in treatment and mass drug administration
LF Chaves, JH Huber, O Rojas Salas, M Ramirez Rojas, LM Romero, JM Gutierrez Alvarado, TA Perkins, M Prado, RM Rodriguez
Microorganisms 8:984
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Wastewater-based epidemiology: global collaborative to maximize contributions in the fight against COVID-19
A Bivins, D North, A Ahmad, W Ahmed, E Alm, F Been, P Bhattacharya, L Bijlsma, AB Boehm, J Brown, G Buttiglieri, V Calabro, A Carducci, A Castiglioni, Z Gurol, S Chakraborty, F Costa, S Curcio, F de los Reyes, J Vela, K Farkas, X Fernandez-Casi, C Gerba, D Gerrity, R Girones, R Gonzalez, E Haramoto, A Harris, P Holden, M Islam, D Jones, B Kasprzyk-Hordern, M Kitajima, N Kotlarz, M Kumar, K Kuroda, G La Rosa, F Malpei, M Mautus, S McLellan, G Medema, J Meschke, J Mueller, R Newton, D Nilsson, R Noble, A van Nuijs, J Peccia, TA Perkins, A Pickering, J Rose, G Sanchez, A Smith, L Stadler, C Stauber, K Thomas, T van der Voorn, K Wigginton, K Zhu, K Bibby
Environmental Science and Technology
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Mapping global variation in human mobility
MUG Kraemer, A Sadilek, Q Zhang, NA Marchal, G Tuli, EL Cohn, Y Hswen, TA Perkins, DL Smith, RC Reiner, JS Brownstein
Nature Human Behavior
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Modeling human migration across spatial scales in Colombia
AS Siraj, A Sorichetta, G España, AJ Tatem, TA Perkins
PLOS ONE 15:e0232702
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Optimizing the deployment of ultra-low volume and indoor residual spraying for dengue outbreak response
SM Cavany, G España, AL Lloyd, LA Waller, U Kitron, H Astete, WH Elson, GM Vazquez-Prokopec, TW Scott, AC Morrison, RC Reiner Jr., TA Perkins
PLOS Computational Biology 16:e1007743
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Ecological dynamics impacting bluetongue virus transmission in North America
CE Mayo, EG McDermott, J Kopanke, M Stenglein, J Lee, C Mathiason, M Carpenter, K Reed, TA Perkins
Frontiers in Veterinary Science
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Aggregated mobility data could help fight COVID-19
CO Buckee, S Balsari, J Chan, M Crosas, F Dominici, U Gasser, YH Grad, B Grenfell, ME Halloran, MUG Kraemer, M Lipsitch, CJE Metcalf, LA Meyers, TA Perkins, M Santillana, SV Scarpino, C Viboud, A Wesolowski, A Schroeder
Science doi:10.1126/eabb8021
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The basic reproductive number for disease systems with multiple coupled heterogeneities
A Lloyd, U Kitron, TA Perkins, GM Vazquez-Prokopec, L Waller
Mathematical Biosciences 321:108294
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2019
Dengue illness impacts daily human mobility patterns in Iquitos, Peru
KL Schaber, VA Paz-Soldan, AC Morrison, WHD Elson, AL Rothman, CN Mores, H Astete-Vega, TW Scott, LA Waller, U Kitron, JP Elder, CM Barker, TA Perkins, GM Vazquez-Prokopec
PLOS Neglected Tropical Diseases 13:e0007756
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Pre-vaccination screening strategies for the use of the CYD-TDV dengue vaccine: a meeting report
A Wilder-Smith, PG Smith, R Luo, C Kelly-Cirino, D Curry, H Larson, A Durbin, M Chu, P Tharmaphornpilas, LC Ng, AMC Sartori, EJA Luna, DJ Gubler, G España, IK Yoon, S Flasche
Vaccine 37 5137-5146
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Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic
N Grubaugh, S Saraf, K Gangavarapu, A Watts, AL Tan, RJ Oidtman, JT Ladner, G Oliveira, NL Matteson, MUG Kraemer, CBF Vogels, A Hentoff, D Bhatia, D Stanek, B Scott, V Landis, I Stryker, M Cone, E Kopp, A Cannons, L Heberlein-Larson, S White, L Gillis, M Ricciardi, J Kwal, P Lichtenberger, D Magnani, D Watkins, G Palacios, DH Hamer, GeoSentinel Surveillance Network, L Gardner, TA Perkins, G Baele, K Khan, A Morrison, S Isern, SF Michael, KG Andersen
Cell 178:1057-1071 doi:10.1016/j.cell.2019.07.018
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Heterogeneous local dynamics revealed by classification analysis of spatially disaggregated time series data
TA Perkins*, I Rodriguez-Barraquer*, C Manore*, AS Siraj, G España, CM Barker, MA Johansson, RC Reiner, Jr.*
Epidemics 100357
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Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure
G España, Y Yao, KB Anderson, MC Fitzpatrick, DL Smith, AC Morrison, A Wilder-Smith, TW Scott, TA Perkins
PLOS Neglected Tropical Diseases 13:e0007482
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Downgrading disease transmission risk estimates using terminal importations
SJ Fox, SE Bellan, TA Perkins, MA Johansson, LA Meyers
PLOS Neglected Tropical Diseases 13:e0007395
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Estimating the impact of city-wide Aedes aegypti population control: an observational study in Iquitos, Peru
RC Reiner, Jr., S Stoddard, G Vazquez-Prokopec, H Astete, TA Perkins, M Sihuincha, J Stancil, DL Smith, T Kochel, E Halsey, U Kitron, AC Morrison, TW Scott
PLOS Neglected Tropical Diseases 13:e0007255
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An agent-based model of dengue virus transmission shows how uncertainty about breakthrough infections influences vaccination impact projections
TA Perkins*, RC Reiner, Jr.*, G España*, QA ten Bosch, A Verma, K Liebman, VA Paz-Soldan, JP Elder, AC Morrison, ST Stoddard, U Kitron, GM Vazquez-Prokopec, TW Scott, DL Smith
PLOS Computational Biology 15:e1006710
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Inter-annual variation in seasonal dengue epidemics driven by multiple interacting factors in Guangzhou, China
RJ Oidtman, S Lai, Z Huang, J Yang, AS Siraj, RC Reiner, Jr., AJ Tatem, TA Perkins, H Yu
Nature Communications 10:1148
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Spatial sorting as the spatial analogue of natural selection
BL Phillips, TA Perkins
Theoretical Ecology 12:155-163
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Past and future spread of the arbovirus vectors Aedes aegypti and Aedes albopictus
MUG Kraemer*, RC Reiner, Jr.*, OJ Brady*, JP Messina*, M Gilbert*, DM Pigott, D Yi, K Johnson, L Earl, LB Marczak, S Shirude, ND Weaver, D Bisanzio, TA Perkins, S Lai, X Lu, P Jones, GE Coelho, RG Carvalho, W Van Bortel, C Marsboom, G Hendrickx, F Schaffner, CG Moore, HH Nax, L Bengtsson, E Wetter, AJ Tatem, JS Brownstein, DL Smith, L Lambrechts, S Cauchemez, C Linard, NR Faria, OG Pybus, TW Scott, Q Liu, H Yu, GRW Wint, SI Hay, N Golding
Nature Microbiology
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Letter to the editor in response to 'Reconstruction and prediction of viral disease epidemics'
TA Perkins
Epidemiology and Infection 147:398
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Biased efficacy estimates in phase-III dengue vaccine trials due to heterogeneous exposure and differential detectability of primary infections across trial arms
G España, C Hogea, A Guignard, QA ten Bosch, AC Morrison, DL Smith, TW Scott, A Schmidt, TA Perkins
PLOS ONE 14:e0210041
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Arbovirus coinfection and co-transmission: a neglected public health concern?
CBF Vogels*, C Ruckert*, SM Cavany*, TA Perkins, GD Ebel, ND Grubaugh
PLOS Biology 17:e3000130
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2018
Mapping malaria by combining parasite genomic and epidemiologic data
A Wesolowski, A Taylor, H-H Chang, R Verity, S Tessema, J Bailey, TA Perkins, D Neafsey, B Greenhouse, CO Buckee
BMC Medicine 16:190
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Local and regional dynamics of chikungunya virus transmission in Colombia: the role of mismatched spatial heterogeneity
SM Moore, QA ten Bosch, AS Siraj, KJ Soda, G España, A Campo, S Gómez, D Salas, B Raybaud, E Wenger, P Welkhoff, TA Perkins
BMC Medicine 16:152
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Exploring scenarios of chikungunya mitigation with a data-driven agent-based model of the 2014-2016 outbreak in Colombia
G España, J Grefenstette, TA Perkins, C Torres, A Campo Carey, H Diaz, F de la Hoz, DS Burke, WG van Panhuis
Scientific Reports 8:12201
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Implementation and applications of EMOD, an individual-based multi-disease modeling platform
A Bershtyn, J Gerardin, D Bridenbecker, CW Lorton, J Bloedow, RS Baker, G Chabot-Couture, Y Chen, T Fischle, K Frey, JS Gauld, H Hu, AS Izzo, DJ Klein, D Lukacevic, KA McCarthy, JC Miller, AL Ouedraogo, TA Perkins, J Steinkraus, QA ten Bosch, HF Ting, S Titova, BG Wagner, PA Welkhoff, EA Wenger, CN Wiswell
Pathogens and Disease 76:fty059
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Model-based analysis of experimental data from interconnected, row-configured huts elucidates multifaceted effects of a volatile chemical on Aedes aegypti mosquitoes
QA ten Bosch, F Castro-Llanos, H Manda, AC Morrison, JP Grieco, NL Achee, TA Perkins
Parasites and Vectors 11:365
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Inferences about spatiotemporal variation in dengue virus transmission are sensitive to assumptions about human mobility: a case study using geolocated tweets from Lahore, Pakistan
MUG Kraemer, D Bisanzio, RC Reiner, Jr., R Zakar, JB Hawkins, CC Freifeld, DL Smith, SI Hay, JS Brownstein, TA Perkins
EPJ Data Science 7:16
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Contributions from the silent majority dominate dengue virus transmission
QA ten Bosch, HE Clapham, L Lambrechts, V Duoung, P Buchy, BM Althouse, AL Loyd, LA Waller, AC Morrison, U Kitron, GM Vazquez-Prokopec, TW Scott, TA Perkins
PLOS Pathogens 14:e1006965
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Spatiotemporal incidence of Zika and associated environmental drivers for the 2015-2016 epidemic in Colombia
AS Siraj, I Rodriguez-Barraquer, CM Barker, N Tejedor-Garavito, D Harding, C Lorton, D Lukacevic, G Oates, G España, MUG Kraemer, C Manore, MA Johansson, AJ Tatem, RC Reiner, Jr., TA Perkins
Scientific Data 5:180073
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DTK-Dengue: A new agent-based model of dengue virus transmission dynamics
KJ Soda, SM Moore, G España, J Bloedow, B Raybaud, B Althouse, MA Johansson, E Wenger, P Welkhoff, TA Perkins*, QA ten Bosch*
bioRxiv doi:10.1101/376533
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2017
Assessing the population at risk of Zika virus in Asia - is the emergency really over?
AS Siraj, TA Perkins
BMJ Global Health 2:e000309
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Temperature modulates dengue virus epidemic growth rates through its effects on reproduction numbers and generation intervals
AS Siraj, RJ Oidtman, JH Huber, MUG Kraemer, OJ Brady, MA Johansson, TA Perkins
PLOS Neglected Tropical Diseases 11:e0005797
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Retracing Zika's footsteps across the Americas with computational modeling
TA Perkins
Proceedings of the National Academy of Sciences 114:5558-5560
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Preliminary results of models to predict areas in the Americas with increased likelihood of Zika virus transmission in 2017
Zika Modeling and Projections for Vaccination Trials Collaboration (in alphabetical order): J Asher, C Barker, G Chen, D Cummings, M Chinazzi, S Daniel-Wyman, M Fischer, N Ferguson, D Follman, ME Halloran, M Johansson, K Kugeler, J Kwan, J Lessler, IM Longini, S Merler, A Monaghan, A Pastore y Piontti, TA Perkins, DR Prevots, RC Reiner, Jr., L Rossi, I Rodriguez-Barraquer, AS Siraj, K Sun, A Vespignanni, Q Zhang
bioRxiv doi:10.1101/187591
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2016
The long-term safety, public health impact, and cost-effectiveness of routine vaccination with a recombinant, live-attenuated dengue vaccine (Dengvaxia): A model comparison study
S Flasche*, M Jit*, I Rodriguez-Barraquer*, L Coudeville*, M Recker*, K Koelle*, G Milne*, TJ Hladish*, TA Perkins*, DAT Cummings, I Dorigatti, DJ Laydon, G España, J Kelso, I Longini, J Lourenco, CAB Pearson, RC Reiner, Jr., L Mier-y-Teran-Romero, K Vannice, N Ferguson
PLOS Medicine 13:e1002181
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Pokemon Go and exposure to mosquito-borne diseases: How not to catch 'em all
RJ Oidtman, RC Christofferson, QA ten Bosch, G España, MUG Kraemer, AJ Tatem, CM Barker, TA Perkins
PLOS Currents Outbreaks
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Quantitative, model-based estimates of variability in the generation and serial intervals of Plasmodium falciparum malaria
JH Huber, GL Johnston, B Greenhouse, DL Smith, TA Perkins
Malaria Journal 15:490
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After the games are over: life-history trade-offs drive dispersal attenuation following range expansion
TA Perkins, C Boettiger, BL Phillips
Ecology and Evolution doi:10.1002/ece3.2314
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Model-based projections of Zika virus infections in childbearing women in the Americas
TA Perkins, AS Siraj, C Warren Ruktanonchai, MUG Kraemer, AJ Tatem
Nature Microbiology 1:16126
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Calling in sick: impacts of fever on intra-urban human mobility
TA Perkins, VA Paz Soldan, ST Stoddard, AC Morrison, BM Forshey, KC Long, ES Halsey, TJ Kochel, JP Elder, U Kitron, TW Scott, GM Vazquez-Prokopec
Proceedings of the Royal Society B 283:20160390
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Quantifying the epidemiological impact of vector control on dengue
RC Reiner, Jr., N Achee, R Barrera, TR Burkot, DD Chadee, G Devine, T Endy, D Gubler, J Homback, I Kleinschmidt, A Lenhart, S Lindsay, I Longini, M Mondy, AC Morrison, TA Perkins, GM Vazquez-Prokopec, P Reiter, S Ritchie, DL Smith, D Strickman, TW Scott
PLOS Neglected Tropical Diseases 10:e0004588
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Coupled heterogeneities and their impact on parasite transmission and control
GM Vazquez-Prokopeck, TA Perkins, LA Waller, AL Lloyd, RC Reiner, Jr., TW Scott, U Kitron
Trends in Parasitology 32:356-367
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Vectorial capacity and vector control: reconsidering sensitivity to parameters for malaria elimination
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, ME Sinka, CL Moyes, PA Eckhoff, TW Scott, SW Lindsay, SI Hay, DL Smith
Transactions of the Royal Society of Tropical Medicine and Hygiene 110:107-117
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2015
Mapping residual transmission for malaria elimination
RC Reiner, Jr., A Le Menach, S Kunene, N Ntshalintshali, M Hsiang, TA Perkins, B Greenhouse, AJ Tatem, JM Cohen, DL Smith
eLife 4:e09520
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Big city, small world: density, contact rates, and transmission of dengue across Pakistan
MUG Kraemer, TA Perkins, DAT Cummings, R Zakar, SI Hay, DL Smith, RC Reiner, Jr.
Journal of the Royal Society Interface 12:20150468
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A critical assessment of vector control for dengue prevention
NL Achee, F Gould, TA Perkins, RC Reiner, Jr., AC Morrison, SA Ritchie, DJ Gubler, R Teyssou, TW Scott
PLOS Neglected Tropical Diseases 9:e0003655
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The changing epidemiology of dengue in China, 1990-2014: a descriptive analysis of 25 years of nationwide surveillance data
S Lai, Z Huang, H Zhou, KL Anders, TA Perkins, W Yin, Y Li, D Mu, Q Chen, Z Zhang, Y Qiu, L Wang, H Zhang, L Zeng, X Ren, M Geng, Z Li, AJ Tatem, SI Hay, H Yu
BMC Medicine 13:100
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Adult vector control, mosquito ecology, and malaria transmission
OJ Brady, HCJ Godfray, AJ Tatem, PW Gething, JM Cohen, FE McKenzie, TA Perkins, RC Reiner, Jr., LS Tusting, TW Scott, SW Lindsay, SI Hay, DL Smith
International Health 7:121-129
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Estimating drivers of autochthonous transmission of chikungunya virus in its invasion of the Americas
TA Perkins, CJE Metcalf, BT Grenfell, AJ Tatem
PLOS Currents Outbreaks
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2014 and before
See Alex's Google Scholar page for a list of his publications prior to forming his lab at Notre Dame.
